|
| Status |
Public on Mar 01, 2017 |
| Title |
10_a_28_48 |
| Sample type |
SRA |
| |
|
| Source name |
Rep A - Autotrophic Batch Culture
|
| Organism |
Galdieria sulphuraria |
| Characteristics |
strain: 074W
temperature: 28°C
sampling: C-28.1
genotype: wild type
truseq adapter index: 12
adapter sequence: CTTGTA
|
| Growth protocol |
42°C/28°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions using 2xGS Medium (M. B. Allen (1959). Studies with cyanidium caldarium, an anomalously pigmented chlorophyte. Archiv für Mikrobiologie, vol. 32, no. 3, p. 270–277.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Roboklon’s Universal RNA Purification Kit by following the “plant tissue samples” protocol (Roboklon, Berlin - Germany). RNA quality and concentration was assessed using a Nanodrop photospectrometer ND-1000 (Peqlab Biotechnologie GmbH, Erlangen -Germany).
The samples were synthetized to Illumina HiSeq2000 compatible RNA-Seq libraries strictly following "Illumina TruSeq RNA Sample Prep v2 LS Protocol" (Illumina, San Diego - USA). All reagents were scaled by 2/3 to the volume proposed in the protocol. The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA). The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA). The libraries were sequenced in paired-end mode (2x100bp) on two lanes with an Illumina HiSeq2000 sequencer at the BMFZ (Biologisch-Medizinisches Forschungszentrum, Düsseldorf - Germany).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sampled after move to 28C for 48 hours
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,
Genome_build: PRJNA13023; https://www.ncbi.nlm.nih.gov/genome/405?genome_assembly_id=29037
Supplementary_files_format_and_content: tab-delimited text files include raw counts per gene
|
| |
|
| Submission date |
Oct 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andreas PM Weber |
| E-mail(s) |
aweber@hhu.de
|
| Organization name |
Heinrich-Heine-University
|
| Department |
Institute for Plant Biochemistry
|
| Street address |
Universitätsstr. 1
|
| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22605 |
| Series (1) |
| GSE89169 |
Selection for transcript diversity in the extremophile Galdieria sulphuraria results in retention of the splicing machinery |
|
| Relations |
| BioSample |
SAMN05941450 |
| SRA |
SRX2268192 |
